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Job request: 11673

Organisation:
University of Liverpool
Workspace:
flucats_test
ID:
zo64j4ylmfb5siqg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    test_action
    Status:
    Status: Succeeded
    Job identifier:
    r7etjxgulcj6wchp

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  test_action:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_test --index-date-range "2020-03-01 to 2020-03-01 by month" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_test_*.csv.gz

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2021-03-07 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  # gives until 2022-03-27. Only have ONS deaths until 2021-07-01
  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-14 to 2022-03-20 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz
  

  generate_study_population_end:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_end.csv.gz

  join_cohorts_weekly:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/input_20*.csv.gz
        --rhs output/input_end.csv.gz
        --output-dir output/joined
    needs: [
      generate_study_population_1,
      generate_study_population_2,
      generate_study_population_end]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz


  generate_dataset_report:
    run: >
      dataset-report:v0.0.24
        --input-files output/joined/input_2022-03-20.csv.gz
        --output-dir output/joined
    needs: [join_cohorts_weekly]
    outputs:
      moderately_sensitive:
        dataset_report: output/joined/input_2022-03-20.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:40:40

These timestamps are generated and stored using the UTC timezone on the EMIS backend.

Job request

Status
Succeeded
Backend
EMIS
Workspace
flucats_test
Requested by
Louis Fisher
Branch
study-def-performance
Force run dependencies
No
Git commit hash
596ade0
Requested actions
  • test_action

Code comparison

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  • No previous job request available for comparison